About 12,000 people who did not need to fill in a self-assessment tax return have been sent out penalty notices by mistake, HMRC has admitted.

The 10.5 million taxpayers in self-assessment had until 2 February to file their forms, and HMRC has written to 650,000 who failed to do so to fine them £100 and warn them that from 1 May they face penalties of £10 a day.

However, it said among these letters were 12,000 to people who had called the taxman and been told they did not need to fill in a form, perhaps because their circumstances had changed since the previous year.

A spokesman for HMRC said these people would receive follow-up letters telling them there had been a mistake, but in the meantime they could put them in the bin.

"We are very sorry and can reassure these customers that we know who they are and that this letter is incorrect – they do not owe a penalty. We are writing to all of them to apologise and to explain this error."

HMRC said that since the start of February it had removed 130,000 people from self-assessment, and that people who did not think they needed to file a return for the 2010/11 tax year could still get in touch. If it was found that they were correct, they could be removed from self-assessment and any penalties would be scrapped.

The spokesman added: "It is very unfortunate that this process error has taken the shine off the good news that we have taken 130,000 people out of self-assessment."